Polyploidization altered gene functions in cotton (Gossypium spp.)

Abstract

Cotton (Gossypium spp.) is an important crop plant that is widely grown to produce both natural textile fibers and cottonseed oil. Cotton fibers, the economically more important product of the cotton plant, are seed trichomes derived from individual cells of the epidermal layer of the seed coat. It has been known for a long time that large numbers of genes determine the development of cotton fiber, and more recently it has been determined that these genes are distributed across At and Dt subgenomes of tetraploid AD cottons. In the present study, the organization and evolution of the fiber development genes were investigated through the construction of an integrated genetic and physical map of fiber development genes whose functions have been verified and confirmed. A total of 535 cotton fiber development genes, including 103 fiber transcription factors, 259 fiber development genes, and 173 SSR-contained fiber ESTs, were analyzed at the subgenome level. A total of 499 fiber related contigs were selected and assembled. Together these contigs covered about 151 Mb in physical length, or about 6.7% of the tetraploid cotton genome. Among the 499 contigs, 397 were anchored onto individual chromosomes. Results from our studies on the distribution patterns of the fiber development genes and transcription factors between the At and Dt subgenomes showed that more transcription factors were from Dt subgenome than At, whereas more fiber development genes were from At subgenome than Dt. Combining our mapping results with previous reports that more fiber QTLs were mapped in Dt subgenome than At subgenome, the results suggested a new functional hypothesis for tetraploid cotton. After the merging of the two diploid Gossypium genomes, the At subgenome has provided most of the genes for fiber development, because it continues to function similar to its fiber producing diploid A genome ancestor. On the other hand, the Dt subgenome, with its non-fiber producing D genome ancestor, provides more transcription factors that regulate the expression of the fiber genes in the At subgenome. This hypothesis would explain previously published mapping results. At the same time, this integrated map of fiber development genes would provide a framework to clone individual full-length fiber genes, to elucidate the physiological mechanisms of the fiber differentiation, elongation, and maturation, and to systematically study the functional network of these genes that interact during the process of fiber development in the tetraploid cottons.

Figure 1. Integrated physical and genetic map of contigs 7.

Example of a tetraploid cotton BAC/BIBAC contig anchored to Dt subgenome chromosome 24. This contig consisted of 42 clones from two source libraries and was estimated to span 1,032 kb. This integrated contig contains three parts: Part A is the genetic markers (NAU1197 and NAU1262, [40]), EST (GA__Ea0001B19, [44]), and five development genes (P3B01, P3B04, P3B06, and P3B08, [48]) that were anchored to contigs by Overgo hybridization; Part B is the overlapped continued BAC clones, the contig. The arrow indicated clone is the positive clone of the marker or fiber genes; Part C is the EST Unigenes that were anchored to contigs by both Overgo hybridization and sequence comparison, same unigene names were used as original paper (Udall et al., 2006). The clone names contain 9 characters, the first three letters are library name (CBV stands for Cotton B amHI, and vector V04541; CHE stands for Cotton H ind III vector pECBAC1), the following three digits are the microtitter plate number, and the last three characters are the clone position in a microtitter plate. Such as “CBV056D16”, it means that this clone came from cotton TM-1 BamHI, vector V04541 library, and located in D row column 16 in microtiter plate number 56.

Figure 2. Part of the contig map of the gene distribution patterns between subgenomes At and Dt.

Numbers on the left are the genetic distances. BAC-contigs are listed on the right. Ctg stands for contig; the following 5 digits are the contig numbers. If a contig is labeled as “at” after the contig name, it means that this contig is anchored to subgenome At only, same as “dt”. The contig that is not labeled either “at” or “dt” is shared between subgenomes At and Dt. The detailed mapping information is available in the supplemental Figure S1.

Figure 3. Workflow of this research.

Schematic flowchart of anchoring the fiber development genes and transcript factors into subgenomes At and Dt.